The Dark Dance

This is a new collaboration with artist Alice Dunsheath that brings to light the vast diversity, and activity of the human microbiome. Each individual video here is of an actual member of my own microbiome, observed at 1000x magnification using a Differential Interference Contrast (DIC) microscope. The work illustrates differences in cell type, size and shape, and also motility. Some of the bacteria here are non-motile and seem happy to drift along on microscopic currents, whilst others move with a frenzied intent.

A massive thank you to Alice Dunsheath for her help with this.

Biogenic Textile Designs: three colours

This is a work from a new series of explorations that continue my fascination with purely biogenic designs. The colours and patterns derive directly from nature, and explore its complexity, natural laws, and inherent creativity. Each design also reflects, and is generated by a story, much like a traditional tapestry might be. In this work though, the colours and designs are generated solely by naturally pigmented bacteria, as they move through a silk fabric and interact with each other.

 

Just after inoculation, the living red, purple and blue bacteria clearly visible at their corresponding sites of inoculation

Just after inoculation, the living red, purple and blue bacteria are clearly visible at their corresponding sites of inoculation

Here is the story of this particular design. Three cultures of pigmented bacteria have been inoculated onto silk. These living bacterial cultures are Serratia marcescens (red), Chromobacterium violaceum (purple) and Arthrobacter polychromogenes (blue). The red and purple bacterial strains are motile, and thus the bacteria begin to move and swarm through the textile colouring it with their corresponding pigments wherever they are present. The blue living pigment, however, is not motile however, and thus can only remain where it was inoculated. After 24 hours of incubation red and purple have moved, but whilst blue has also grown it has remained at its site of inoculation.

After 24 hours purple and red have moved as expected (they are motile) and blue remains stationary as its's non-motile.

After 24 hours purple and red have moved as expected (they are motile) and blue remains stationary as it’s non-motile.

After 60 hours of incubation red has begun to overcome blue, but the purple pigmented bacterium cannot approach it. It’s thus likely that blue produces an antibiotic the red is resistant to, but that purple isn’t.

After 60 hours of incubation red has begun to overcome blue, but the purple pigmented bacterium cannot approach it. It's thus likely that blue produces an antibiotic the red is resistant to, but that purple isn't.

After 60 hours of incubation red has begun to overcome blue, but the purple pigmented bacterium cannot approach it. It’s thus likely that blue produces an antibiotic the red is resistant to, but that purple isn’t.

Biogenic Textile Designs: the cloth that listens

Close up of the biogenic textile design, the purple colour/design only appears where the two species of bacteria are communicating

Close up of the biogenic textile design, the purple colour/design only appears where the two species of bacteria are communicating

Close up of the biogenic textile design, the purple colour/design only appears where the two species of bacteria are communicating

Close up of the biogenic textile design, the purple colour/design only appears where the two species of bacteria are communicating

 

This is a work from a new series of explorations that continue my fascination with purely biogenic designs. The colours and patterns here all derive directly from nature, and explore its complexity, natural laws, and inherent creativity. Each design also reflects, and is generated by a story, much like a traditional tapestry might be. In this work though, the colours and designs are generated by a genetically modified bacterium that produces a purple pigment when it detects communication signals for other bacteria.

Here is the story of this particular textile design. Bacteria possess complex chemical communication systems that endow them with a form of social intelligence. In the simplest sense they use these systems to signal their presence to other related bacteria and through this census-taking, ensure that their communities express only specific functions at particular and appropriate population densities. These systems also allow bacterial communities  to operate a form of bacterial democaracy in that individual cells can vote on issues affecting the entire population,  and influence decisions. The same processes allow bacteria also to function as multi-cellular organisms.

Chromobacterium violaceum is a common soil bacterium that produces striking purple colonies. In relation to the concept above, the expression of this colour is dependent on bacterial communication so that when a small number of bacteria are present its cells will be white but it turns purple when it receives many communication signals from other bacteria. When it grows in colonies, individual bacteria of this species are continually sending and receiving signals and consequently the colony will be purple. I have a genetically modified version of C. violaceum called CV026 that is effectively mute. It has been modified so that it can receive chemical communication signals and respond to them, but it cannot send them, so that it only turns purple if it detects a communication signal from another type of  bacterium. In this sense, it is a unique sensor for bacterial communication giving a striking and direct visualization of this phenomenon.

 

In this work the sensor strain has been inoculated onto the silk textile as a series of three squares, and then on both sides of these squares, a long streak of the bacterium Erwinia carotovora has been added.

The textile just after inoculation. The squares are of the reporter bacterium CV026 and the vertical streaks are E. carotovora, the signal producer. As the bacteria haven't yet grown or interacted there is no colour development yet.

The textile just after inoculation. The squares are of the reporter bacterium CV026 and the vertical streaks are E. carotovora, the signal producer. As the bacteria haven’t yet grown or interacted there is no colour development yet.

 

After 24 hours incubation. The bacteria are moving, interacting and communicated to generate an emerging purple glyph

After 24 hours incubation. The bacteria are moving, interacting and communicated to generate an emerging purple glyph

Both bacteria are initially colourless but E. carotovora produces a communication signal that CV026 can detect and respond to, and as the bacteria move through the fabric and where the bacteria then meet and interact, CV026 begins to produce its purple pigment. The area of purple colouration and its design directly reflects this interaction.

 

The fully developed glyph or  textile design after 60 hours incubation.

The fully developed glyph or textile design after 60 hours incubation.

BioGenic Textile Designs: A BioBatik in Purple and Red

This is a work from a new series of explorations that continue my fascination with purely biogenic designs. The colours and patterns derive directly from nature, and explore its complexity, natural laws, and inherent creativity. Each design also reflects, and is generated by a story, much like a traditional tapestry might be. In this work though, the colours and designs are generated solely by naturally pigmented bacteria, as they move through a silk fabric, interact with each other, and respond to various challenges offered to them.

The textile just after inoculation with the different coloured streaks of the two bacteria clearly visible

The textile just after inoculation with the different coloured streaks of the two bacteria clearly visible

Here is the story of this particular design. Two cultures of pigmented bacteria have been inoculated onto silk in the form of a long streak at either end. The two living cultures are Serratia marcescens (red) and Chromobacterium violaceum (purple). In addition, towards the centre of the silk, four drops of the antibiotic cloxacillin have been introduced onto the fabric to provide a challenge, and in the hope that much like wax does in the Batik Process, these spots might act as a resist (the antibiotic is colourless so these spots are invisible at first).

Both bacterial strains are motile, and thus the bacteria begin to move and swarm through the textile colouring it with their corresponding pigments wherever they are present. In terms of the territory occupied it can be seen the red coloured bacterium has gained the greater share of the silk, and could thus be considered to be the faster moving, and most aggressive species. In the greater territory occupied by the red pigmented bacterium Serratia marcescens, however, there are two undyed circles within the silk, and these correspond to the location of the spots of the antibiotic cloxacillin. This red coloured bacterium is clearly sensitive to the antibiotic and it cannot grow in its presence to colour the silk red.

After 24 hours of incubation. The two bacteria have moved. Red has moved the furthest but the white zones where the four antibiotic spots are clearly visible. The upper zones will later be taken over by the purple coloured bacterium

After 24 hours of incubation. The two bacteria have moved. Red has moved the furthest but the white zones where the four antibiotic spots are, are clearly visible. The upper zones will later be taken over by the purple coloured bacterium

After 24 hours of incubation. The antibiotic spots are clearly visible.

After 24 hours of incubation. The antibiotic spots are clearly visible.

After 24 hours of incubation. The antibiotic spots are clearly visible.

After 24 hours of incubation. The antibiotic spots are clearly visible.

There are two other spots of antibiotic above those that caused the white circles, and the antibiotic has still prevented the growth of Serratia marcescens in these, but here, these Serratia-free zones have been occupied by the purple bacterium, Chromobacterium violaceum, which must be resistant to the antibiotic and which has exploited the antibiotic vulnerability of its competitor, to establish a foothold in its territory.

After 72 hours of incubation. The urple bacterium has now occupied the upper antibiotic zones where the red bacterium could not grow.

After 72 hours of incubation. The urple bacterium has now occupied the upper antibiotic zones where the red bacterium could not grow.

The dried and sterlised textile.

The dried and sterlised textile.

The Search for Microbiomal Scents

Finger tip. Thursday. Dominated by moulds.

Finger tip. Thursday. Dominated by moulds.

Finger tip. Wednesday. Dominated by the soil bacterium Bacillus mycoides. A colony from my microbiome is producing an antibiotic that inhibits the growth of this bacterium and produces a zone of no growth.

Finger tip. Wednesday. Dominated by the soil bacterium Bacillus mycoides. A colony from my microbiome is producing an antibiotic that inhibits the growth of this bacterium and produces a zone of no growth.

Feet

Feet

Smell can evoke the richest of memories, and through this sense our most intimate and affecting moments can be reached more readily than through any other channel. The project is inspired by my own experiences in medical microbiology, and how we were taught to presumtively identify bacterial pathogens on the basis of the aroma that they generate. To this day I can still remember the moment, when in an undergraduate microbiology lab class, the late Joyce Fraser told me that Haemophilus influenza when grown on blood agar smells of semen! She was of course quite correct. Here are some other bacterial aroma notes:

Eikenella corrodens: bleach

Staphyloccocus aureus: skin-like smell with a secondary smell of bread.

Pseudomonas aeruginosa: initial smell of grapes with a secondary smell of tortillas

Group F Beta Hemolytic Streptococcus: strong buttery smell

Stenotrophomonas: ammonia

Staphylococcus epidermidis: body odour

Streptococcus intermedius: butterscotch

Proteus vulgaris: burnt chocolate

Flavobacterium odoratum and Alcaligenes faecalis (formerly Alcaligenes odorans) freshly cut apple

Streptomyces coelicolor: freshly dug soil/autumnal woodlands

Gluconoacetobacter species: vinegar

Clostridium perfringens: horse shit

I’m attempting to generate a highly personalized perfume, that smells of me, or as the many bacteria of my microbiome generate my unique bodily aroma, that also is derived from these prokaryotic cells. This is a first screen to isolate bacteria from my microbiome.

Chalk from the Anthropocene: lime mud

A lump of lime mud. A precursor to chalk made by a culture of Coccolithophora and the sedimentation by its dead cells.

A lump of lime mud. A precursor to chalk made by a culture of Coccolithophora and the sedimentation of  its dead cells.

A lump of lime mud. A precursor to chalk made by a culture of Coccolithophora and the sedimentation by its dead cells.

A lump of lime mud. A precursor to chalk made by a culture of Coccolithophora and the sedimentation of its dead cells.

A lump of lime mud. A precursor to chalk made by a culture of Coccolithophora and the sedimentation by its dead cells.

A lump of lime mud. A precursor to chalk made by a culture of Coccolithophora and the sedimentation of  its dead cells.

Here some lumps of the lime mud have been trapped between two microscope slides and mixed with an acid. This treatment liberates the trapped carbon dioxide which can be seen as bubbles.

Here some lumps of the lime mud have been trapped between two microscope slides and mixed with an acid. This treatment liberates the trapped carbon dioxide which can be seen as bubbles.

Chalk is formed when lime mud is transformed into rock by geological processes. Usually, this calcium carbonate rich mud accumulates on the seafloor, more  calcareous sediment builds up on top of it, and as the sea floor subsides, the lime mud is subjected to heat and pressure. These processes remove water and compact the sediment into rock. The lime mud itself is formed from the skeletons of microscopic plankton, which rain down on the sea floor from the sunlit waters above and a group of microbes called the Coccolithophores are considered to be the most important group of chalk forming plankton. Each individual Coccolithophore cell has a spherical skeleton made from a number of calcium carbonate rich discs called coccoliths which after death, fall to the floor of the oceans to generate lime mud. Most of chalk edifices that we are familiar with formed during the Cretaceous period, between 100 and 60 million years ago, and reflect a period when global temperatures, concentrations of greenhouse gases and sea levels were exceptionally high.

We now live in an age when humans and our activities are having a significant global impact on the Earth’s ecosystems and its climate. The Anthropocene is an informal term for the proposed geological epoch that began when human activities began to have such a global impact including increases in global temperatures, concentrations of greenhouse gases and sea levels. This work explores the parallel between the Cretaceous period and the Anthropocene, in that is seeks to make chalk of Anthropocene origin and which also will  include locked in anthropogenic carbon dioxide from the burning of fossil fuels. For a period of six months, air has been bubbled through a culture of mixed Coccolithophora species, and I have been successful in the first steps of chalk production, that is the production of a lime mud, the essential precursor to chalk.